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After Massena's victory in the Second Battle of Zurich the alliance between Russia and Austria ended. Despite this it did not end the war and when Napoleon came back from Egypt and proclaimed himself First Consul, the French prospects of victory improved even more. However, Napoleon needed time in order to bring his troops in Italy so he ordered Massena to hold Nice and Genoa at all costs until he arrived.

Initially the French had about 60,000 soldiers, but due to disease they were reduced to about 36,000 fighting men. Austrian commander Melas had around 120,000 soldiers available in Italy. After the first engagements, despite the bravery of the French commanded by Suchet and Soult, Genoa was soon cut off from any outside help and by 6 April the French were surrounded not only by land, but also by sea where a strong British squadron had just taken up positions. Nevertheless the French morale remained high and Massena was determined to hold on.

Genoa was defended both by nature and by strong fortifications, but Massena planned a more offensive strategy. On 7 April he ordered an attack on Monte Ratti, which resulted in the Austrians being thrown out of the Apennines and the French capturing about 1,500 prisoners, including General-Major Konstantin Ghilian Karl d'Aspré. On April 9 Massena started a desperate operation to unite with the rest of the French forces commanded by Suchet. Although Massena was cut off with only 1,200 soldiers against 10,000 Austrians he endured their attacks and with the help of Soult captured another 4,000 prisoners. After this battle the French finally shut themselves in the city. Other desperately fought battles soon followed, especially those for Fort Quezzi and Fort Richelieu, inflicting further heavy casualties on the Austrians. This was followed by a battle for the possession of Mount Creto where the French were victorious again and the Austrians halted all further actions.

In the meantime, Bonaparte marched with the Army of the Reserve, not to the relief of Genoa, but to Milan where he spent six days. By the end of May, plague had spread throughout Genoa and the civilian population was in revolt. Negotiations were begun for the exchange of prisoners early in June, but the citizens and some of the garrison clamoured for capitulation. Unknown to Masséna, the Austrian general, Peter Ott, had been ordered to raise the siege because Bonaparte had crossed Great St. Bernard Pass and was now threatening the main Austrian army. Describing the situation at Genoa, Ott requested and received permission to continue the siege. On 4 June, with one day's rations remaining, Masséna's negotiator finally agreed to evacuate the French army from Genoa. However, "if the word capitulation was mentioned or written", Masséna threatened to end all negotiations.[1]

Two days later, a few of the French left the city by sea, but the bulk of Masséna's starving and exhausted troops marched out of the city with all their equipment and followed the road along the coast toward France, ending one of the most remarkable sieges in modern military history. The siege was an astonishing demonstration of tenacity, ingenuity, courage, and daring that garnered additional laurels for Masséna and placed him in a category previously reserved for Bonaparte alone.[2]

The gruelling siege of some sixty days had ended but it played an important role in Bonaparte's strategy. By forcing the Austrians to deploy vast forces against him at Genoa, Masséna made it possible for Bonaparte to cross the Great St. Bernard Pass, surprise the Austrians, and ultimately defeat General Michael Melas's army at Marengo before sufficient reinforcements could be transferred from the siege site. Less than three weeks after the evacuation, Bonaparte wrote to Masséna, "I am not able to give you a greater mark of the confidence I have in you than by giving you command of the first army of the Republic [Army of Italy]."[3] The Austrians also recognized the significance of Masséna's defense; the Austrian chief of staff declared firmly, "You won the battle, not in front of Alessandria but in front of Genoa."[4]